2DLK - JenaLib

NMR Structure - model 1

NMR Structure - model 1, sites

NMR Structure - all models

collapse

expand

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Description

Title :   SOLUTION STRUCTURE OF THE FIRST AND THE SECOND ZF-C2H2 DOMAINS OF ZINC FINGER PROTEIN 692

Authors :   H. P. Zhang, T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   20 Apr 06 (Deposition) - 20 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Zf-C2H2 Domain, Zinc Finger Protein 692, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. P. Zhang, T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of The First And The Second Zf-C2H2 Domains Of Zinc Finger Protein 692
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - NOVEL PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P050302-82
	Expression System Vector Type	:	PLASMID
	Fragment	:	ZF-C2H2 DOMAIN, RESIDUES 8-73
	Gene	:	ZNF692
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL FREE PROTEIN SYNTHESIS
	Synonym	:	ZINC FINGER PROTEIN 692

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 2)

NMR Structure (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Sites (2, 2)

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:10 , CYS A:15 , HIS A:28 , HIS A:33	BINDING SITE FOR RESIDUE ZN A 201
2	AC2	SOFTWARE	CYS A:41 , CYS A:46 , HIS A:59 , HIS A:63	BINDING SITE FOR RESIDUE ZN A 401

SS Bonds (0, 0)

(no "SS Bond" information available for 2DLK)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2DLK)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2DLK)

PROSITE Motifs (1, 3)

NMR Structure (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_FINGER_C2H2_1	PS00028	Zinc finger C2H2 type domain signature.	ZN692_HUMAN	330-353 361-383 391-411 419-439 450-471	3	A:10-33 A:41-63 A:71-78 - -

Exons (5, 5)

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1g	ENST00000306601	1g	ENSE00001274045	chr1:249153271-249153117	155	ZN692_HUMAN	-	0	0	-	-
1.2h	ENST00000306601	2h	ENSE00002192734	chr1:249152520-249152330	191	ZN692_HUMAN	1-60	60	0	-	-
1.2s	ENST00000306601	2s	ENSE00001169785	chr1:249152058-249152027	32	ZN692_HUMAN	60-71	12	0	-	-
1.2ac	ENST00000306601	2ac	ENSE00001274082	chr1:249151696-249151433	264	ZN692_HUMAN	71-159	89	0	-	-
1.3b	ENST00000306601	3b	ENSE00001169729	chr1:249150761-249150713	49	ZN692_HUMAN	159-175	17	0	-	-
1.4b	ENST00000306601	4b	ENSE00001433115	chr1:249150621-249150487	135	ZN692_HUMAN	175-220	46	0	-	-
1.5c	ENST00000306601	5c	ENSE00002155973	chr1:249150145-249149924	222	ZN692_HUMAN	220-294	75	1	A:1-2	2
1.5j	ENST00000306601	5j	ENSE00001699190	chr1:249149834-249149757	78	ZN692_HUMAN	294-320	27	1	A:2-7	6
1.6b	ENST00000306601	6b	ENSE00001752900	chr1:249149657-249149579	79	ZN692_HUMAN	320-346	27	1	A:8-26	19
1.7b	ENST00000306601	7b	ENSE00001764543	chr1:249148250-249148136	115	ZN692_HUMAN	347-385	39	1	A:27-65	39
1.9	ENST00000306601	9	ENSE00001693020	chr1:249144980-249144881	100	ZN692_HUMAN	385-418	34	1	A:65-79 (gaps)	19
1.10k	ENST00000306601	10k	ENSE00001657197	chr1:249144715-249144205	511	ZN692_HUMAN	418-519	102	0	-	-

Sequences/Alignments

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:79
 aligned with ZN692_HUMAN | Q9BU19 from UniProtKB/Swiss-Prot  Length:519

    Alignment length:111
                                   302       312       322       332       342       352       362       372       382       392       402 
          ZN692_HUMAN   293 ASTGSQAQSAPTPAWDEDTAQIGPKRIRKAAKRELMPCDFPGCGRIFSNRQYLNHHKKYQHIHQKSFSCPEPACGKSFNFKKHLKEHMKLHSDTRDYICEFCARSFRTSSN 403
               SCOP domains -----------------------------------d2dlka1 A:8-37                d2dlka2 A:38-73                     ---------- SCOP domains
               CATH domains ------------------------------------------------------------------2dlkA02 A:39-64           ------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......----------------------------ee........ee.hhhhhhhhhhhh......ee........ee.hhhhhhhhhhhhhh..........----.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------ZINC_FINGER_C2H2_1      -------ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C PROSITE
           Transcript 1 (1) 1.-------------------------Exon 1.6b  PDB: A:8-26     Exon 1.7b  PDB: A:27-65                ------------------ Transcript 1 (1)
           Transcript 1 (2) -Exon 1.5j  PDB: A:2-7      ----------------------------------------------------------------Exon 1.9            Transcript 1 (2)
                 2dlk A   1 GSSGSSG----------------------------MPCDFPGCGRIFSNRQYLNHHKKYQHIHQKSFSCPEPACGKSFNFKKHLKEHMKLHSDTRDYICEFSG----PSSG  79
                                  |  -         -         -     |  12        22        32        42        52        62        72  |    |78 
                                  7                            8                                                                 75   76

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 2)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: beta-beta-alpha zinc fingers (183)

Superfamily: beta-beta-alpha zinc fingers (183)

Family: Classic zinc finger, C2H2 (162)

Protein domain: Zinc finger protein 692, ZNF692 (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d2dlka1	A:8-37
1b	d2dlka2	A:38-73

CATH Domains (1, 1)

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Double Stranded RNA Binding Domain (204)

Homologous Superfamily: Classic Zinc Finger (45)

Human (Homo sapiens) (4)

2dlkA02

A:39-64

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2DLK)

Gene Ontology (6, 6)

NMR Structure(hide GO term definitions)

Chain A (ZN692_HUMAN | Q9BU19)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Visualization

Interactive Views

NMR Structure
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2dlk)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - model 1, sites PNG format \| NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2dlk
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ZN692_HUMAN \| Q9BU19
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ZN692_HUMAN \| Q9BU19
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	ZN692_HUMAN \| Q9BU19	:	2d9h

Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2DLK)